[English] 日本語
Yorodumi
- EMDB-32050: Al-bound structure of the AtALMT1 mutant M60A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32050
TitleAl-bound structure of the AtALMT1 mutant M60A
Map dataAl-bound structure of the AtALMT1 mutant M60A
Sample
  • Complex: Al-bound protein sample of the AtALMT1 mutant M60A
    • Protein or peptide: Aluminum-activated malate transporter 1
  • Ligand: ACETIC ACID
  • Ligand: ALUMINUM ION
KeywordsALMT1 / Aluminum Resistance / malate transport / TRANSPORT PROTEIN
Function / homologymalate transmembrane transport / malate transmembrane transporter activity / Aluminum-activated malate transporter / Aluminium activated malate transporter / response to aluminum ion / monoatomic ion transmembrane transport / plasma membrane / Aluminum-activated malate transporter 1
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang J
Funding support China, 9 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
Ministry of Science and Technology (MoST, China)2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31870724 China
National Natural Science Foundation of China (NSFC)82030108 China
National Natural Science Foundation of China (NSFC)31872796 China
National Natural Science Foundation of China (NSFC)81571127 China
National Natural Science Foundation of China (NSFC)31730006 China
National Natural Science Foundation of China (NSFC)31600606 China
CitationJournal: Cell Res / Year: 2022
Title: Structural basis of ALMT1-mediated aluminum resistance in Arabidopsis.
Authors: Jiangqin Wang / Xiafei Yu / Zhong Jie Ding / Xiaokang Zhang / Yanping Luo / Ximing Xu / Yuan Xie / Xiaoxiao Li / Tian Yuan / Shao Jian Zheng / Wei Yang / Jiangtao Guo /
Abstract: The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron ...The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron microscopy (cryo-EM) structures of Arabidopsis thaliana ALMT1 (AtALMT1) in the apo, malate-bound, and Al-bound states at neutral and/or acidic pH at up to 3.0 Å resolution. The AtALMT1 dimer assembles an anion channel and each subunit contains six transmembrane helices (TMs) and six cytosolic α-helices. Two pairs of Arg residues are located in the center of the channel pore and contribute to malate recognition. Al binds at the extracellular side of AtALMT1 and induces conformational changes of the TM1-2 loop and the TM5-6 loop, resulting in the opening of the extracellular gate. These structures, along with electrophysiological measurements, molecular dynamic simulations, and mutagenesis study in Arabidopsis, elucidate the structural basis for Al-activated malate transport by ALMT1.
History
DepositionOct 14, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7voj
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32050.png

Downloads & links

-
Map

FileDownload / File: emd_32050.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAl-bound structure of the AtALMT1 mutant M60A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 180 pix.
= 182.52 Å		1.01 Å/pix.
x 180 pix.
= 182.52 Å		1.01 Å/pix.
x 180 pix.
= 182.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.10789047 - 0.15441944
Average (Standard dev.)-0.00008028117 (±0.005481161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 182.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z182.520182.520182.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1080.154-0.000

-
Supplemental data

-
Sample components

-
Entire : Al-bound protein sample of the AtALMT1 mutant M60A

EntireName: Al-bound protein sample of the AtALMT1 mutant M60A
Components
  • Complex: Al-bound protein sample of the AtALMT1 mutant M60A
    • Protein or peptide: Aluminum-activated malate transporter 1
  • Ligand: ACETIC ACID
  • Ligand: ALUMINUM ION

-
Supramolecule #1: Al-bound protein sample of the AtALMT1 mutant M60A

SupramoleculeName: Al-bound protein sample of the AtALMT1 mutant M60A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Organ: root / Tissue: root apex / Location in cell: cell membrane
Molecular weightTheoretical: 120 kDa/nm

-
Macromolecule #1: Aluminum-activated malate transporter 1

MacromoleculeName: Aluminum-activated malate transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 56.773551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVA TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST ...String:
MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVA TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST VVIGGVSCIL ISIFVCPVWA GQDLHSLLAS NFDTLSHFLQ DFGDEYFEAR EKGDYKVVEK RKKNLERYKS VL DSKSDEE ALANYAEWEP PHGQFRFRHP WKQYVAVGAL LRQCAYRIDA LNSYINSDFQ IPVDIKKKLE TPLRRMSSES GNS MKEMSI SLKQMIKSSS SDIHVSNSQA ACKSLSTLLK SGILNDVEPL QMISLMTTVS MLIDIVNLTE KISESVHELA SAAR FKNKM RPTVLYEKSD SGSIGRAMPI DSHEDHHVVT VLHDVDNDRS NNVDDSRGGS SQDSCHHVAI KIVDDNSNHE KHEDG EIHV HTLSNGHLQL EGGSSGGWSH PQFEK

UniProtKB: Aluminum-activated malate transporter 1

-
Macromolecule #2: ACETIC ACID

MacromoleculeName: ACETIC ACID / type: ligand / ID: 2 / Number of copies: 4 / Formula: ACY
Molecular weightTheoretical: 60.052 Da
Chemical component information

ChemComp-ACY:
ACETIC ACID

-
Macromolecule #3: ALUMINUM ION

MacromoleculeName: ALUMINUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: AL
Molecular weightTheoretical: 26.982 Da
Chemical component information

ChemComp-AL:
ALUMINUM ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 5
Component:
ConcentrationFormulaName
150.0 mMNaclSodium chloride
50.0 mMNaAc-HAcSodium acetate-acetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3586060
Details: about 1,000 particles were manually picked from the micrographs for 2D classification initially. Class averages representing projections of AtALMT1 in different orientations were selected ...Details: about 1,000 particles were manually picked from the micrographs for 2D classification initially. Class averages representing projections of AtALMT1 in different orientations were selected and used as templates for automated particle picking
Startup modelType of model: OTHER
Details: the ALMT1M60A/Al/pH5 model was built according to the reference ALMT1apo/pH5 model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 216946
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50 / Avg.num./class: 5 / Software - Name: RELION (ver. 3.0)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more